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(-) Description

Title :  CRYSTAL STRUCTURE OF ATP-SULFURYLASE DOMAIN OF HUMAN PAPS SYNTHETASE 1
 
Authors :  N. Sekulic, A. Lavie
Date :  07 Jul 07  (Deposition) - 11 Nov 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Atp-Sulfurylase, Paps-Synthetase, Monomer-Dimer Equillibrium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Sekulic, I. Paarmann, M. Konrad, A. Lavie
Atp-Sulfurylase Domain Of Human Bifunctional Paps-Synthetase Oscillates Between Dimeric And Monomeric Forms
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'- PHOSPHOSULFATE SYNTHETASE 1
    Chains: A, B
    EC Number: 2.7.7.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-RB
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SULFATE ADENYLYLTRANSFERASE DOMAIN, RESIDUE 220- 624
    Gene: PAPSS1, ATPSK1, PAPSS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PAPS SYNTHETASE 1, PAPSS 1, SULFURYLASE KINASE 1, SK1, SK 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ADX2Ligand/IonADENOSINE-5'-PHOSPHOSULFATE
2K2Ligand/IonPOTASSIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:314 , ASP A:374BINDING SITE FOR RESIDUE K A1001
2AC2SOFTWAREHIS B:314 , ASP B:374BINDING SITE FOR RESIDUE K B1002
3AC3SOFTWAREPHE A:418 , GLN A:419 , LEU A:420 , ARG A:421 , ASN A:422 , HIS A:428 , LEU A:431 , MET A:495 , VAL A:520 , GLY A:521 , ARG A:522 , PRO A:524 , ALA A:525 , ARG A:561 , VAL A:562 , ALA A:563 , HOH A:1073 , HOH A:1098 , HOH A:1100 , HOH A:1188 , HOH A:1235BINDING SITE FOR RESIDUE ADX A 100
4AC4SOFTWAREPHE B:418 , GLN B:419 , LEU B:420 , ARG B:421 , ASN B:422 , HIS B:428 , LEU B:431 , MET B:495 , VAL B:520 , GLY B:521 , ARG B:522 , PRO B:524 , ALA B:525 , ARG B:561 , VAL B:562 , ALA B:563 , HOH B:1018 , HOH B:1046 , HOH B:1049 , HOH B:1068BINDING SITE FOR RESIDUE ADX B 100

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QJF)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:276 -Pro A:277
2Thr B:276 -Pro B:277

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014065L270FPAPS1_HUMANPolymorphism1127008A/BL270F
2UniProtVAR_014064S587LPAPS1_HUMANPolymorphism1127014A/BS587L
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QJF)

(-) Exons   (7, 14)

Asymmetric/Biological Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002651741aENSE00000935008chr4:108641608-108641276333PAPS1_HUMAN1-20200--
1.3ENST000002651743ENSE00000935007chr4:108622441-108622327115PAPS1_HUMAN21-59390--
1.4cENST000002651744cENSE00000736237chr4:108615162-108614927236PAPS1_HUMAN59-137790--
1.5cENST000002651745cENSE00000736234chr4:108608333-108608195139PAPS1_HUMAN138-184470--
1.6ENST000002651746ENSE00000736231chr4:108603289-108603171119PAPS1_HUMAN184-223400--
1.7bENST000002651747bENSE00000841651chr4:108581228-108581115114PAPS1_HUMAN224-261382A:233-261
B:232-261		29
30
1.8ENST000002651748ENSE00000841650chr4:108578163-108578052112PAPS1_HUMAN262-299382A:262-299
B:262-299		38
38
1.9ENST000002651749ENSE00000841649chr4:108576056-108575851206PAPS1_HUMAN299-367692A:299-367
B:299-367		69
69
1.10bENST0000026517410bENSE00001217423chr4:108574782-108574647136PAPS1_HUMAN368-413462A:368-413
B:368-413		46
46
1.11ENST0000026517411ENSE00001217417chr4:108566226-108565958269PAPS1_HUMAN413-502902A:413-502
B:413-502		90
90
1.12aENST0000026517412aENSE00001217412chr4:108553016-108552787230PAPS1_HUMAN503-579772A:503-579
B:503-579		77
77
1.13ENST0000026517413ENSE00001217468chr4:108535543-108534822722PAPS1_HUMAN579-624462A:579-622
B:579-622		44
44

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:390
 aligned with PAPS1_HUMAN | O43252 from UniProtKB/Swiss-Prot  Length:624

    Alignment length:390
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622
          PAPS1_HUMAN   233 EVKELYVPENKLHLAKTDAETLPALKINKVDMQWVQVLAEGWATPLNGFMREREYLQCLHFDCLLDGGVINLSVPIVLTATHEDKERLDGCTAFALMYEGRRVAILRNPEFFEHRKEERCARQWGTTCKNHPYIKMVMEQGDWLIGGDLQVLDRVYWNDGLDQYRLTPTELKQKFKDMNADAVFAFQLRNPVHNGHALLMQDTHKQLLERGYRRPVLLLHPLGGWTKDDDVPLMWRMKQHAAVLEEGVLNPETTVVAIFPSPMMYAGPTEVQWHCRARMVAGANFYIVGRDPAGMPHPETGKDLYEPSHGAKVLTMAPGLITLEIVPFRVAAYNKKKKRMDYYDSEHHEDFEFISGTRMRKLAREGQKPPEGFMAPKAWTVLTEYYKSLE 622
               SCOP domains d2qjfa1 A:233-392 automated matches                                                                                                                             d2qjfa2 A:393-622 automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhh..eee.hhhhhhhhhhhhhh......ee.hhhhhhhhhhhhee.....ee......eeehhhhhhhhh...eeeeee..eeeeeeeeeeeee.hhhhhhhhhhh.....hhhhhhhhh...eeeeeeeee.........hhhhh.hhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhh...hhh.eee.........hhhhhhhhhhhhhhhh...eeee...................hhhhhhhhhh......eeee...eeee....eeee.hhhhhh.ee..hhhhhhhhhh..........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------F----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.7b  PDB: A:233-261    Exon 1.8  PDB: A:262-299              --------------------------------------------------------------------Exon 1.10b  PDB: A:368-413 UniProt: 368-413   -----------------------------------------------------------------------------------------Exon 1.12a  PDB: A:503-579 UniProt: 503-579                                  ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------Exon 1.9  PDB: A:299-367 UniProt: 299-367                            ---------------------------------------------Exon 1.11  PDB: A:413-502 UniProt: 413-502                                                ----------------------------------------------------------------------------Exon 1.13  PDB: A:579-622 UniProt: 579-624   Transcript 1 (2)
                 2qjf A 233 EVKELYVPENKLHLAKTDAETLPALKINKVDMQWVQVLAEGWATPLNGFMREREYLQCLHFDCLLDGGVINLSVPIVLTATHEDKERLDGCTAFALMYEGRRVAILRNPEFFEHRKEERCARQWGTTCKNHPYIKMVMEQGDWLIGGDLQVLDRVYWNDGLDQYRLTPTELKQKFKDMNADAVFAFQLRNPVHNGHALLMQDTHKQLLERGYRRPVLLLHPLGGWTKDDDVPLMWRMKQHAAVLEEGVLNPETTVVAIFPSPMMYAGPTEVQWHCRARMVAGANFYIVGRDPAGMPHPETGKDLYEPSHGAKVLTMAPGLITLEIVPFRVAAYNKKKKRMDYYDSEHHEDFEFISGTRMRKLAREGQKPPEGFMAPKAWTVLTEYYKSLE 622
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622


Chain B from PDB  Type:PROTEIN  Length:391
 aligned with PAPS1_HUMAN | O43252 from UniProtKB/Swiss-Prot  Length:624

    Alignment length:391
                                   241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621 
          PAPS1_HUMAN   232 YEVKELYVPENKLHLAKTDAETLPALKINKVDMQWVQVLAEGWATPLNGFMREREYLQCLHFDCLLDGGVINLSVPIVLTATHEDKERLDGCTAFALMYEGRRVAILRNPEFFEHRKEERCARQWGTTCKNHPYIKMVMEQGDWLIGGDLQVLDRVYWNDGLDQYRLTPTELKQKFKDMNADAVFAFQLRNPVHNGHALLMQDTHKQLLERGYRRPVLLLHPLGGWTKDDDVPLMWRMKQHAAVLEEGVLNPETTVVAIFPSPMMYAGPTEVQWHCRARMVAGANFYIVGRDPAGMPHPETGKDLYEPSHGAKVLTMAPGLITLEIVPFRVAAYNKKKKRMDYYDSEHHEDFEFISGTRMRKLAREGQKPPEGFMAPKAWTVLTEYYKSLE 622
               SCOP domains d2qjfb1 B:232-392 automated matches                                                                                                                              d2qjfb2 B:393-622 automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) PUA_2-2qjfB03 B:232-386                                                                                                                                    ------ATP-sulfurylase-2qjfB01 B:393-618                                                                                                                                                                                                 ---- Pfam domains (1)
           Pfam domains (2) PUA_2-2qjfB04 B:232-386                                                                                                                                    ------ATP-sulfurylase-2qjfB02 B:393-618                                                                                                                                                                                                 ---- Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhhhhhhh.eee.hhhhhhhhhhhhh..........hhhhhhhhhhhhee.....ee......eeehhhhhhhhh...eeeeee..eeeeeeeeeeeee.hhhhhhhhhhh.....hhhhhhhhh...eeeeeeeee.........hhhhh.hhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhh...hhh.eee..........hhhhhhhhhhhhhhh...eeee...................hhhhhhhhhh......eeee...eeee....eeee.hhhhhh.ee..hhhhhhhhhhh.........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------F----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7b  PDB: B:232-261     Exon 1.8  PDB: B:262-299              --------------------------------------------------------------------Exon 1.10b  PDB: B:368-413 UniProt: 368-413   -----------------------------------------------------------------------------------------Exon 1.12a  PDB: B:503-579 UniProt: 503-579                                  ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.9  PDB: B:299-367 UniProt: 299-367                            ---------------------------------------------Exon 1.11  PDB: B:413-502 UniProt: 413-502                                                ----------------------------------------------------------------------------Exon 1.13  PDB: B:579-622 UniProt: 579-624   Transcript 1 (2)
                 2qjf B 232 YEVKELYVPENKLHLAKTDAETLPALKINKVDMQWVQVLAEGWATPLNGFMREREYLQCLHFDCLLDGGVINLSVPIVLTATHEDKERLDGCTAFALMYEGRRVAILRNPEFFEHRKEERCARQWGTTCKNHPYIKMVMEQGDWLIGGDLQVLDRVYWNDGLDQYRLTPTELKQKFKDMNADAVFAFQLRNPVHNGHALLMQDTHKQLLERGYRRPVLLLHPLGGWTKDDDVPLMWRMKQHAAVLEEGVLNPETTVVAIFPSPMMYAGPTEVQWHCRARMVAGANFYIVGRDPAGMPHPETGKDLYEPSHGAKVLTMAPGLITLEIVPFRVAAYNKKKKRMDYYDSEHHEDFEFISGTRMRKLAREGQKPPEGFMAPKAWTVLTEYYKSLE 622
                                   241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QJF)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)
(-)
Clan: PUA (42)
(-)
Family: PUA_2 (11)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PAPS1_HUMAN | O43252)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004020    adenylylsulfate kinase activity    Catalysis of the reaction: ATP + adenylylsulfate = ADP + 3'-phosphoadenosine 5'-phosphosulfate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0004781    sulfate adenylyltransferase (ATP) activity    Catalysis of the reaction: ATP + sulfate = diphosphate + adenylylsulfate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0050428    3'-phosphoadenosine 5'-phosphosulfate biosynthetic process    The chemical reactions and pathways resulting in the formation of 3'-phosphoadenosine 5'-phosphosulfate, a naturally occurring mixed anhydride. It is an intermediate in the formation of a variety of sulfo compounds in biological systems.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
    GO:0000103    sulfate assimilation    The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PAPS1_HUMAN | O43252: 1x6v 1xjq 1xnj 2ofw 2ofx 2pey 2pez

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2QJF)